Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003) Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time. The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla
[Bioc-devel] Warnings in build for BioCor
8 messages · Lluís Revilla, Matthias Döring, Robert Castelo +1 more
DearLluis, how is your namespace defined? Do you use 'import' or 'importFrom' to load the package in question? If you are currently using 'import' to load all exports from the package, you could switch to 'importFrom' and exclude the function that causes the problems and then use the double-colon operator when referring to the package's function. Kind regards ?Matthias
On 02/28/2018 11:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003) Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time. The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla [[alternative HTML version deleted]]
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Matthias D?ring Max Planck Institute for Informatics Campus E1 4 66123 Saarbr?cken phone: +49 681 9325 3122 fax: +49 681 9325 3099 web: www.mpi-inf.mpg.de/~mdoering
Lluis, something you can do in you NAMESPACE to follow the advice below from Matthias if you are importing the functionality of a whole package is: import(pkgyouneed, except=functionmethodyoudefine) in this way, you're importing everything except that particular function or method that you are defining in your own package. cheers, robert.
On 28/02/2018 12:51, Matthias D?ring wrote:
DearLluis, how is your namespace defined? Do you use 'import' or 'importFrom' to load the package in question? If you are currently using 'import' to load all exports from the package, you could switch to 'importFrom' and exclude the function that causes the problems and then use the double-colon operator when referring to the package's function. Kind regards ?Matthias On 02/28/2018 11:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003) Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time. The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla ????[[alternative HTML version deleted]]
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Dear Matthias and Robert, My namespace doesn't import that package. It is mentioned in the Description file in Suggests, and on the same vignette it is and loaded but after the line where the error is reported. The error is reported on lines 143-148 (BioCor.Rmd) and the library is loaded on line 260. But I might end up using the double colon to avoid the error. Cheers, Llu?s
On 28 February 2018 at 14:26, Robert Castelo <robert.castelo at upf.edu> wrote:
Lluis, something you can do in you NAMESPACE to follow the advice below from Matthias if you are importing the functionality of a whole package is: import(pkgyouneed, except=functionmethodyoudefine) in this way, you're importing everything except that particular function or method that you are defining in your own package. cheers, robert. On 28/02/2018 12:51, Matthias D?ring wrote:
DearLluis, how is your namespace defined? Do you use 'import' or 'importFrom' to load the package in question? If you are currently using 'import' to load all exports from the package, you could switch to 'importFrom' and exclude the function that causes the problems and then use the double-colon operator when referring to the package's function. Kind regards Matthias On 02/28/2018 11:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003) Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time. The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On 02/28/2018 05:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003)
This means that 'another package' is on the search() path. It only gets there if your package attaches it, directly or indirectly. Maybe another package that you attach previously import'ed it, but now depends on it? To narrow this down, step through your vignette code until you see the offending package on the search() path. Maybe you can avoid attaching the intermediate package, or put your package in front of the others on the search path by loading your package last in the vignette. If you're running into these problems, and you're intimately familiar with your package, then one can imagine that users will also run into this problem and the suggestion to mangle your package function names starts to sound appealing.
Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time.
The next Bioconductor release has not been announced (we try to tie these to the R release schedule, and the release of R-3.5 has not yet been announced), but will likely be at the end of April. Martin
The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla [[alternative HTML version deleted]]
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Actually, looking at your github repository, I see you have two vignettes, you have renamed one from vignette2.Rmd to BioCor_advanced.Rmd, and that this vignette now collates before the original one. I believe that vignettes are built in the same R process, so the packages loaded in the first vignette are available (and conflict with) packages loaded in the second. Martin
On 02/28/2018 08:53 AM, Martin Morgan wrote:
On 02/28/2018 05:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003)
This means that 'another package' is on the search() path. It only gets there if your package attaches it, directly or indirectly. Maybe another package that you attach previously import'ed it, but now depends on it? To narrow this down, step through your vignette code until you see the offending package on the search() path. Maybe you can avoid attaching the intermediate package, or put your package in front of the others on the search path by loading your package last in the vignette. If you're running into these problems, and you're intimately familiar with your package, then one can imagine that users will also run into this problem and the suggestion to mangle your package function names starts to sound appealing.
Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time.
The next Bioconductor release has not been announced (we try to tie these to the R release schedule, and the release of R-3.5 has not yet been announced), but will likely be at the end of April. Martin
The End Of Life page of Bioconductor only talks about errors not warnings, and I couldn't find if this has been discussed previously in the archive. I would like to know if I can leave the development version as is (until I find a solution) or should I aim to correct the warning for the next release? Many thanks, Llu?s Revilla ????[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
Thanks Martin for looking into it. I think that is the reason of the problem, the timeline of the errors building certainly match. I couldn't find this documented in Writing R Extensions, is this behavior documented somewhere? Llu?s On 28 February 2018 at 15:03, Martin Morgan <martin.morgan at roswellpark.org> wrote:
Actually, looking at your github repository, I see you have two vignettes, you have renamed one from vignette2.Rmd to BioCor_advanced.Rmd, and that this vignette now collates before the original one. I believe that vignettes are built in the same R process, so the packages loaded in the first vignette are available (and conflict with) packages loaded in the second. Martin On 02/28/2018 08:53 AM, Martin Morgan wrote:
On 02/28/2018 05:31 AM, Llu?s Revilla wrote:
Dear bioconductor core, The development version of my package hosted in Github cannot be build. It seems that another package is loaded when it shouldn't and masks the functions that are used in the vignette. (In case anyone wants to help here is the link to the StackOverflow question: https://stackoverflow.com/q/49002455/2886003)
This means that 'another package' is on the search() path. It only gets there if your package attaches it, directly or indirectly. Maybe another package that you attach previously import'ed it, but now depends on it? To narrow this down, step through your vignette code until you see the offending package on the search() path. Maybe you can avoid attaching the intermediate package, or put your package in front of the others on the search path by loading your package last in the vignette. If you're running into these problems, and you're intimately familiar with your package, then one can imagine that users will also run into this problem and the suggestion to mangle your package function names starts to sound appealing.
Additionally the current version hosted in Bioconductor has a warning in the windows build. Which I hoped to correct for these release. I don't know if I will find a solution on time for the next release (which I expect in three weeks), but I am worried I won't be able to fix it on time.
The next Bioconductor release has not been announced (we try to tie these to the R release schedule, and the release of R-3.5 has not yet been announced), but will likely be at the end of April. Martin
The End Of Life page of Bioconductor only talks about errors not
warnings,
and I couldn't find if this has been discussed previously in the
archive. I
would like to know if I can leave the development version as is (until I
find a solution) or should I aim to correct the warning for the next
release?
Many thanks,
Llu?s Revilla
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
On 02/28/2018 09:35 AM, Llu?s Revilla wrote:
Thanks Martin for looking into it. I think that is the reason of the problem, the timeline of the errors building certainly match. I couldn't find this documented in Writing R Extensions, is this behavior documented somewhere?
I'm not sure if its documented anywhere; the code here https://github.com/wch/r-source/blob/trunk/src/library/tools/R/build.R#L315-L324 seems to involve processing all vignettes with a single call to create a new process. Martin
Llu?s
On 28 February 2018 at 15:03, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>
wrote:
Actually, looking at your github repository, I see you have two
vignettes, you have renamed one from vignette2.Rmd to
BioCor_advanced.Rmd, and that this vignette now collates before the
original one. I believe that vignettes are built in the same R
process, so the packages loaded in the first vignette are available
(and conflict with) packages loaded in the second.
Martin
On 02/28/2018 08:53 AM, Martin Morgan wrote:
On 02/28/2018 05:31 AM, Llu?s Revilla wrote:
Dear bioconductor core,
The development version of my package hosted in Github
cannot be build. It
seems that another package is loaded when it shouldn't and
masks the
functions that are used in the vignette. (In case anyone
wants to help here
is the link to the StackOverflow question:
https://stackoverflow.com/q/49002455/2886003
<https://stackoverflow.com/q/49002455/2886003>)
This means that 'another package' is on the search() path. It
only gets there if your package attaches it, directly or
indirectly. Maybe another package that you attach previously
import'ed it, but now depends on it? To narrow this down, step
through your vignette code until you see the offending package
on the search() path.
Maybe you can avoid attaching the intermediate package, or put
your package in front of the others on the search path by
loading your package last in the vignette.
If you're running into these problems, and you're intimately
familiar with your package, then one can imagine that users will
also run into this problem and the suggestion to mangle your
package function names starts to sound appealing.
Additionally the current version hosted in Bioconductor has
a warning in
the windows build. Which I hoped to correct for these release.
I don't know if I will find a solution on time for the next
release (which
I expect in three weeks), but I am worried I won't be able
to fix it on
time.
The next Bioconductor release has not been announced (we try to
tie these to the R release schedule, and the release of R-3.5
has not yet been announced), but will likely be at the end of April.
Martin
The End Of Life page of Bioconductor only talks about errors
not warnings,
and I couldn't find if this has been discussed previously in
the archive. I
would like to know if I can leave the development version as
is (until I
find a solution) or should I aim to correct the warning for
the next
release?
Many thanks,
Llu?s Revilla
????[[alternative HTML version deleted]]
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